pybiolib 1.2.911__py3-none-any.whl → 1.2.1642__py3-none-any.whl

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Files changed (113) hide show
  1. biolib/__init__.py +33 -10
  2. biolib/_data_record/data_record.py +24 -11
  3. biolib/_index/index.py +51 -0
  4. biolib/_index/types.py +7 -0
  5. biolib/_internal/add_copilot_prompts.py +3 -5
  6. biolib/_internal/add_gui_files.py +59 -0
  7. biolib/_internal/data_record/data_record.py +1 -1
  8. biolib/_internal/data_record/push_data.py +1 -1
  9. biolib/_internal/data_record/remote_storage_endpoint.py +3 -3
  10. biolib/_internal/file_utils.py +48 -0
  11. biolib/_internal/index/__init__.py +1 -0
  12. biolib/_internal/index/index.py +18 -0
  13. biolib/_internal/lfs/cache.py +4 -2
  14. biolib/_internal/push_application.py +89 -23
  15. biolib/_internal/runtime.py +2 -0
  16. biolib/_internal/string_utils.py +13 -0
  17. biolib/_internal/templates/copilot_template/.github/instructions/style-react-ts.instructions.md +47 -0
  18. biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md +19 -0
  19. biolib/_internal/templates/gui_template/.yarnrc.yml +1 -0
  20. biolib/_internal/templates/gui_template/App.tsx +53 -0
  21. biolib/_internal/templates/gui_template/Dockerfile +28 -0
  22. biolib/_internal/templates/gui_template/biolib-sdk.ts +37 -0
  23. biolib/_internal/templates/gui_template/dev-data/output.json +7 -0
  24. biolib/_internal/templates/gui_template/index.css +5 -0
  25. biolib/_internal/templates/gui_template/index.html +13 -0
  26. biolib/_internal/templates/gui_template/index.tsx +10 -0
  27. biolib/_internal/templates/gui_template/package.json +27 -0
  28. biolib/_internal/templates/gui_template/tsconfig.json +24 -0
  29. biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts +49 -0
  30. biolib/_internal/templates/gui_template/vite.config.mts +9 -0
  31. biolib/_internal/templates/init_template/.biolib/config.yml +1 -0
  32. biolib/_internal/templates/init_template/.github/workflows/biolib.yml +6 -1
  33. biolib/_internal/templates/init_template/Dockerfile +2 -0
  34. biolib/_internal/templates/init_template/run.sh +1 -0
  35. biolib/_internal/templates/templates.py +9 -1
  36. biolib/_internal/utils/__init__.py +25 -0
  37. biolib/_internal/utils/job_url.py +33 -0
  38. biolib/_internal/utils/multinode.py +12 -14
  39. biolib/_runtime/runtime.py +15 -2
  40. biolib/_session/session.py +7 -5
  41. biolib/_shared/__init__.py +0 -0
  42. biolib/_shared/types/__init__.py +69 -0
  43. biolib/_shared/types/account.py +12 -0
  44. biolib/_shared/types/account_member.py +8 -0
  45. biolib/{_internal → _shared}/types/experiment.py +1 -0
  46. biolib/_shared/types/resource.py +17 -0
  47. biolib/_shared/types/resource_deploy_key.py +11 -0
  48. biolib/{_internal → _shared}/types/resource_permission.py +1 -1
  49. biolib/{_internal → _shared}/types/user.py +5 -5
  50. biolib/_shared/utils/__init__.py +7 -0
  51. biolib/_shared/utils/resource_uri.py +75 -0
  52. biolib/api/client.py +1 -1
  53. biolib/app/app.py +96 -45
  54. biolib/biolib_api_client/app_types.py +1 -0
  55. biolib/biolib_api_client/biolib_app_api.py +26 -0
  56. biolib/biolib_binary_format/module_input.py +8 -0
  57. biolib/biolib_binary_format/remote_endpoints.py +3 -3
  58. biolib/biolib_binary_format/remote_stream_seeker.py +39 -25
  59. biolib/biolib_logging.py +1 -1
  60. biolib/cli/__init__.py +2 -1
  61. biolib/cli/auth.py +4 -16
  62. biolib/cli/data_record.py +17 -0
  63. biolib/cli/index.py +32 -0
  64. biolib/cli/init.py +93 -11
  65. biolib/cli/lfs.py +1 -1
  66. biolib/cli/run.py +1 -1
  67. biolib/cli/start.py +14 -1
  68. biolib/compute_node/job_worker/executors/docker_executor.py +31 -9
  69. biolib/compute_node/job_worker/executors/docker_types.py +1 -1
  70. biolib/compute_node/job_worker/executors/types.py +6 -5
  71. biolib/compute_node/job_worker/job_storage.py +2 -1
  72. biolib/compute_node/job_worker/job_worker.py +155 -90
  73. biolib/compute_node/job_worker/large_file_system.py +2 -6
  74. biolib/compute_node/job_worker/network_alloc.py +99 -0
  75. biolib/compute_node/job_worker/network_buffer.py +240 -0
  76. biolib/compute_node/job_worker/utilization_reporter_thread.py +2 -2
  77. biolib/compute_node/remote_host_proxy.py +135 -67
  78. biolib/compute_node/utils.py +2 -0
  79. biolib/compute_node/webserver/compute_node_results_proxy.py +188 -0
  80. biolib/compute_node/webserver/proxy_utils.py +28 -0
  81. biolib/compute_node/webserver/webserver.py +64 -19
  82. biolib/experiments/experiment.py +98 -16
  83. biolib/jobs/job.py +128 -31
  84. biolib/jobs/job_result.py +73 -33
  85. biolib/jobs/types.py +1 -0
  86. biolib/sdk/__init__.py +17 -2
  87. biolib/typing_utils.py +1 -1
  88. biolib/utils/cache_state.py +2 -2
  89. biolib/utils/seq_util.py +1 -1
  90. {pybiolib-1.2.911.dist-info → pybiolib-1.2.1642.dist-info}/METADATA +4 -2
  91. pybiolib-1.2.1642.dist-info/RECORD +180 -0
  92. {pybiolib-1.2.911.dist-info → pybiolib-1.2.1642.dist-info}/WHEEL +1 -1
  93. biolib/_internal/llm_instructions/.github/instructions/style-react-ts.instructions.md +0 -22
  94. biolib/_internal/types/__init__.py +0 -6
  95. biolib/_internal/types/account.py +0 -10
  96. biolib/utils/app_uri.py +0 -57
  97. pybiolib-1.2.911.dist-info/RECORD +0 -150
  98. /biolib/{_internal/llm_instructions → _index}/__init__.py +0 -0
  99. /biolib/_internal/{llm_instructions → templates/copilot_template}/.github/instructions/general-app-knowledge.instructions.md +0 -0
  100. /biolib/_internal/{llm_instructions → templates/copilot_template}/.github/instructions/style-general.instructions.md +0 -0
  101. /biolib/_internal/{llm_instructions → templates/copilot_template}/.github/instructions/style-python.instructions.md +0 -0
  102. /biolib/_internal/{llm_instructions → templates/copilot_template}/.github/prompts/biolib_app_inputs.prompt.md +0 -0
  103. /biolib/_internal/{llm_instructions → templates/copilot_template}/.github/prompts/biolib_run_apps.prompt.md +0 -0
  104. /biolib/{_internal → _shared}/types/app.py +0 -0
  105. /biolib/{_internal → _shared}/types/data_record.py +0 -0
  106. /biolib/{_internal → _shared}/types/file_node.py +0 -0
  107. /biolib/{_internal → _shared}/types/push.py +0 -0
  108. /biolib/{_internal/types/resource.py → _shared/types/resource_types.py} +0 -0
  109. /biolib/{_internal → _shared}/types/resource_version.py +0 -0
  110. /biolib/{_internal → _shared}/types/result.py +0 -0
  111. /biolib/{_internal → _shared}/types/typing.py +0 -0
  112. {pybiolib-1.2.911.dist-info → pybiolib-1.2.1642.dist-info}/entry_points.txt +0 -0
  113. {pybiolib-1.2.911.dist-info → pybiolib-1.2.1642.dist-info/licenses}/LICENSE +0 -0
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@@ -1,4 +1,4 @@
1
1
  Wheel-Version: 1.0
2
- Generator: poetry-core 2.1.3
2
+ Generator: poetry-core 2.2.1
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
@@ -1,22 +0,0 @@
1
- ---
2
- applyTo: "**/*.ts,**/*.tsx"
3
- ---
4
-
5
- Apply the [general coding guidelines](./style-general.instructions.md) to all code.
6
-
7
- # General Project Guidelines
8
- - Use yarn instead of npm whenever relevant.
9
- - Prefer using `export default function` over exporting at the end of the file.
10
-
11
- # TypeScript Guidelines
12
- - Use TypeScript for all new code
13
- - Follow functional programming principles where possible
14
- - Use interfaces for data structures prefixed with I like `interface IRecord`
15
- - Prefer immutable data (const, readonly)
16
- - Use optional chaining (?.) and nullish coalescing (??) operators
17
-
18
- # React Guidelines
19
- - Use functional components with hooks
20
- - Follow the React hooks rules (no conditional hooks)
21
- - Prefer one component per file
22
- - Use Tailwindcss for styling
@@ -1,6 +0,0 @@
1
- from .app import * # noqa: F403
2
- from .data_record import * # noqa: F403
3
- from .experiment import * # noqa: F403
4
- from .resource import * # noqa: F403
5
- from .resource_permission import * # noqa: F403
6
- from .resource_version import * # noqa: F403
@@ -1,10 +0,0 @@
1
- from .typing import TypedDict
2
-
3
-
4
- class AccountDict(TypedDict):
5
- uuid: str
6
- handle: str
7
-
8
-
9
- class AccountDetailedDict(TypedDict):
10
- pass
biolib/utils/app_uri.py DELETED
@@ -1,57 +0,0 @@
1
- import re
2
-
3
- from biolib.biolib_errors import BioLibError
4
- from biolib.typing_utils import TypedDict, Optional
5
-
6
-
7
- class SemanticVersion(TypedDict):
8
- major: int
9
- minor: int
10
- patch: int
11
-
12
-
13
- class AppUriParsed(TypedDict):
14
- account_handle_normalized: str
15
- app_name_normalized: Optional[str]
16
- app_name: Optional[str]
17
- resource_name_prefix: Optional[str]
18
- version: Optional[SemanticVersion]
19
-
20
-
21
- def normalize(string: str) -> str:
22
- return string.replace('-', '_').lower()
23
-
24
-
25
- # Mainly copied from backend
26
- def parse_app_uri(uri: str, use_account_as_name_default: bool = True) -> AppUriParsed:
27
- uri_regex = r'^(@(?P<resource_name_prefix>[\w._-]+)/)?(?P<account_handle>[\w-]+)(/(?P<app_name>[\w-]+))?' \
28
- r'(:(?P<version>(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)))?$'
29
-
30
- uri_without_trailing_asterisk_version = uri[:-2] if uri.endswith(':*') else uri
31
- matches = re.search(uri_regex, uri_without_trailing_asterisk_version)
32
- if matches is None:
33
- raise BioLibError(f"Could not parse app uri '{uri}', uri did not match regex")
34
-
35
- resource_name_prefix: Optional[str] = matches.group('resource_name_prefix')
36
- account_handle_normalized: str = normalize(matches.group('account_handle'))
37
- app_name: Optional[str] = matches.group('app_name')
38
-
39
- # Default to account_handle if app_name is not supplied
40
- if app_name:
41
- app_name_normalized = normalize(app_name)
42
- elif use_account_as_name_default:
43
- app_name_normalized = account_handle_normalized
44
- else:
45
- app_name_normalized = None
46
-
47
- return AppUriParsed(
48
- resource_name_prefix=resource_name_prefix.lower() if resource_name_prefix is not None else 'biolib.com',
49
- account_handle_normalized=account_handle_normalized,
50
- app_name_normalized=app_name_normalized,
51
- app_name=app_name if app_name is not None or not use_account_as_name_default else account_handle_normalized,
52
- version=None if not matches.group('version') else SemanticVersion(
53
- major=int(matches.group('major')),
54
- minor=int(matches.group('minor')),
55
- patch=int(matches.group('patch')),
56
- )
57
- )
@@ -1,150 +0,0 @@
1
- biolib/__init__.py,sha256=o0cpNzP7OwPYfdw5Cq-XgsMYooQdQynZTUO3W-LFuKo,10657
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- biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- biolib/_internal/add_copilot_prompts.py,sha256=6gbqYsrTTUFTEEV62fp-UTDwZeJIjDfvywWgtW6AowQ,1967
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- biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
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- biolib/_internal/data_record/data_record.py,sha256=SD3-tKQY2RZv9ZSVNUhd2ISDYV64Fk1Sc642qyf_Vis,4618
7
- biolib/_internal/data_record/push_data.py,sha256=-L3a_7zZzDCXabBu3O4lWPMAMeBbeRPTrBlEM-_5SCI,2693
8
- biolib/_internal/data_record/remote_storage_endpoint.py,sha256=eCptuZ4DMAPnaNCVDvpWXwXGI6Jac9U1N5dqU8Cj95Q,1732
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- biolib/_internal/errors.py,sha256=AokI6Dvaa22B__LTfSZUVdDsm0ye7lgBFv_aD9O_kbs,163
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- biolib/_internal/file_utils.py,sha256=4jT6j7bB21c0JNn5BfnyWQib_zt0CVtJ_TiOFOStRcE,2604
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- biolib/_internal/fuse_mount/__init__.py,sha256=B_tM6RM2dBw-vbpoHJC4X3tOAaN1H2RDvqYJOw3xFwg,55
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- biolib/_internal/fuse_mount/experiment_fuse_mount.py,sha256=08aUdEq_bvqLBft_gSLjOClKDy5sBnMts1RfJf7AP_U,7012
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- biolib/_internal/http_client.py,sha256=9-3HG6LnLwJfrwjCeFj5XigHVH8Dzz6Dpr58IjQJHDo,6221
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- biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjnPpE,35
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- biolib/_internal/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
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